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- PDB-9sg3: X-ray structure of acetylcholine binding protein (AChBP) in compl... -

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Basic information

Entry
Database: PDB / ID: 9sg3
TitleX-ray structure of acetylcholine binding protein (AChBP) in complex with IOTA739
ComponentsAcetylcholine-binding protein
KeywordsCHOLINE-BINDING PROTEIN / Acetylcholine binding protein / ligand gated ion channel / SPR
Function / homology
Function and homology information


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / synapse / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Ig-like domain profile. / Immunoglobulin-like domain
Similarity search - Domain/homology
1,10-PHENANTHROLINE / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCederfelt, D. / Lund, B.A. / Boronat, P. / Hennig, S. / Dobritzsch, D. / Danielson, U.H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675899European Union
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Detection and characterisation of ligand-induced conformational changes in acetylcholine binding proteins using biosensors and X-ray crystallography.
Authors: FitzGerald, E.A. / Cederfelt, D. / Kovryzhenko, D. / Boronat, P. / Lund, B.A. / Dobritzsch, D. / Hennig, S. / Paseiro, P.P. / de Esch, I.J.P. / Danielson, U.H.
History
DepositionAug 21, 2025Deposition site: PDBE / Processing site: PDBE
SupersessionSep 3, 2025ID: 9QM8
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,77719
Polymers234,20010
Non-polymers1,5779
Water3,153175
1
A: Acetylcholine-binding protein
B: Acetylcholine-binding protein
C: Acetylcholine-binding protein
D: Acetylcholine-binding protein
E: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,12410
Polymers117,1005
Non-polymers1,0245
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Acetylcholine-binding protein
G: Acetylcholine-binding protein
H: Acetylcholine-binding protein
I: Acetylcholine-binding protein
J: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6539
Polymers117,1005
Non-polymers5534
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.950, 117.850, 239.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 20 through 174 or resid 181 through 223))
d_2ens_1(chain "B" and (resid 20 through 174 or resid 181 through 223))
d_3ens_1(chain "C" and (resid 20 through 174 or resid 181 through 223))
d_4ens_1(chain "D" and (resid 20 through 174 or resid 181 through 223))
d_5ens_1(chain "E" and (resid 20 through 174 or resid 181 through 223))
d_6ens_1(chain "F" and (resid 20 through 174 or resid 181 through 223))
d_7ens_1(chain "G" and (resid 20 through 174 or resid 181 through 223))
d_8ens_1(chain "H" and (resid 20 through 174 or resid 181 through 223))
d_9ens_1(chain "I" and (resid 20 through 174 or resid 181 through 223))
d_10ens_1(chain "J" and (resid 20 through 174 or resid 181 through 223))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUTHRTHRAA20 - 1741 - 155
d_12SERSERLYSLYSAA181 - 223162 - 204
d_21LEULEUTHRTHRBB20 - 1741 - 155
d_22SERSERLYSLYSBB181 - 223162 - 204
d_31LEULEUTHRTHRCC20 - 1741 - 155
d_32SERSERLYSLYSCC181 - 223162 - 204
d_41LEULEUTHRTHRDD20 - 1741 - 155
d_42SERSERLYSLYSDD181 - 223162 - 204
d_51LEULEUTHRTHREE20 - 1741 - 155
d_52SERSERLYSLYSEE181 - 223162 - 204
d_61LEULEUTHRTHRFF20 - 1741 - 155
d_62SERSERLYSLYSFF181 - 223162 - 204
d_71LEULEUTHRTHRGG20 - 1741 - 155
d_72SERSERLYSLYSGG181 - 223162 - 204
d_81LEULEUTHRTHRHH20 - 1741 - 155
d_82SERSERLYSLYSHH181 - 223162 - 204
d_91LEULEUTHRTHRII20 - 1741 - 155
d_92SERSERLYSLYSII181 - 223162 - 204
d_101LEULEUTHRTHRJJ20 - 1741 - 155
d_102SERSERLYSLYSJJ181 - 223162 - 204

NCS oper:
IDCodeMatrixVector
1given(0.362097921261, -0.112070111331, 0.925378509349), (-0.120813137282, 0.978730205067, 0.165805221718), (-0.924277707877, -0.171835607005, 0.340856630985)38.906555861, 6.84129528736, -0.710930644821
2given(-0.732230310757, -0.318440973607, 0.602025014711), (-0.332834523914, 0.938524529559, 0.0916127016708), (-0.594188481629, -0.133293112142, -0.793204257777)51.7377182364, 9.17647276699, -40.1272689759
3given(-0.757251762812, -0.339685638188, -0.557838179876), (-0.314062815571, 0.938263180394, -0.145006041919), (0.572655494686, 0.0653901485431, -0.817184075273)18.5983322306, 1.94308238648, -64.7636024208
4given(0.292175593484, -0.136613944695, -0.946556946352), (-0.105398684514, 0.979116145941, -0.173846743026), (0.950539078563, 0.150559632282, 0.271674910973)-13.051337573, -2.88525520922, -41.1695809148
5given(-0.999806466445, 0.00583243775902, -0.0187886222009), (-0.00685110902514, -0.998483844223, 0.054617535009), (-0.0184415823494, 0.0547356875825, 0.998330562762)36.6426904756, 14.7800715388, -0.045188970442
6given(-0.346103837417, 0.110121294276, -0.931711025089), (0.0826381825115, -0.985649441672, -0.147194119862), (-0.934549658668, -0.127939355469, 0.332036830496)-2.32309069872, 7.24576868246, -1.3042210189
7given(0.743895659671, 0.322968866748, -0.585072951548), (0.307624828473, -0.942688925191, -0.129246103339), (-0.593284259381, -0.0838373510607, -0.800615442106)-14.3214573475, 3.11278492615, -40.7521136441
8given(0.7370556657, 0.337879721962, 0.585308669973), (0.344160816153, -0.932998343122, 0.105201826774), (0.58163758328, 0.123900707094, -0.803956675759)19.8372480019, 9.1739692265, -65.0692697343
9given(-0.330988608369, 0.132107357852, 0.934341579473), (0.155251047059, -0.96903521006, 0.192010088411), (0.930775834193, 0.20861066048, 0.300229810007)50.6651137351, 15.3187619719, -39.9092002814

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Components

#1: Protein
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 23420.014 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P58154
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-PHN / 1,10-PHENANTHROLINE


Mass: 180.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H8N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350 3% Ammonium sulfate 1.8 M HEPES buffer 0.1M, pH 7.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→49.59 Å / Num. obs: 43398 / % possible obs: 99.89 % / Redundancy: 7.5 % / Biso Wilson estimate: 78.11 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2174 / Net I/σ(I): 8.28
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 1.906 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 4270 / CC1/2: 0.523 / Rrim(I) all: 2.052

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.59 Å / SU ML: 0.5544 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.9419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2693 1999 4.61 %
Rwork0.2476 41375 -
obs0.2486 43374 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.79 Å2
Refinement stepCycle: LAST / Resolution: 3→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16110 0 108 175 16393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004316574
X-RAY DIFFRACTIONf_angle_d0.844322607
X-RAY DIFFRACTIONf_chiral_restr0.05442589
X-RAY DIFFRACTIONf_plane_restr0.00662903
X-RAY DIFFRACTIONf_dihedral_angle_d6.27222213
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.10918435289
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.14458323972
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.21090672393
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS1.09571944346
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.870690546807
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS1.03383288011
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS1.09580107076
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS1.15829428385
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS1.14689992089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.43021390.4352882X-RAY DIFFRACTION99.9
3.08-3.160.43271410.39982915X-RAY DIFFRACTION99.97
3.16-3.250.42371420.37432935X-RAY DIFFRACTION99.97
3.25-3.360.36881400.34912891X-RAY DIFFRACTION99.97
3.36-3.480.34571410.32982921X-RAY DIFFRACTION99.84
3.48-3.620.36241410.28642915X-RAY DIFFRACTION100
3.62-3.780.29391420.25592946X-RAY DIFFRACTION99.9
3.78-3.980.23961420.23672942X-RAY DIFFRACTION99.97
3.98-4.230.25421420.22192936X-RAY DIFFRACTION100
4.23-4.550.23821420.19012950X-RAY DIFFRACTION100
4.55-5.010.20941440.19122980X-RAY DIFFRACTION100
5.01-5.740.21851450.19352985X-RAY DIFFRACTION100
5.74-7.220.22551450.23443009X-RAY DIFFRACTION99.97
7.22-49.590.23351530.2213168X-RAY DIFFRACTION99.49

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